def rearrange(self, savefig=False):
dfs, pool = self.sumxrl()
# Change the question: whether it is more plus? so you need to swap 0 and 1 during a minus reference
pool_labels = pool['allResponses'].index
pool['revResponses'] = pool['allResponses']
for label in pool_labels:
if label.endswith('m'):
pool['revResponses'][label] = 1 - pool['allResponses'][label]
# Combine each two conditions
rearranged = pd.DataFrame(columns=[
'hue', 'intensity', 'response', 'ntrial', 'combinedInten',
'combinedResp', 'combinedN', 'sems', 'fit', 'pse', 'thre'
])
# stupid but straightforward way to combine...
for ii in np.arange(0, len(pool_labels) - 1, 2):
idx = ii // 2
rearranged.loc[idx, 'hue'] = 'hue_' + str(idx + 1)
rearranged.loc[idx, 'intensity'] = np.hstack(
[pool['allIntensities'][ii], pool['allIntensities'][ii + 1]])
rearranged.loc[idx, 'response'] = np.hstack(
[pool['allResponses'][ii], pool['allResponses'][ii + 1]])
rearranged.loc[idx, 'ntrial'] = pool['ntrial'][0] * 2
rearranged.loc[idx, 'combinedInten'], \
rearranged.loc[idx, 'combinedResp'], \
rearranged.loc[idx, 'combinedN'] = data.functionFromStaircase(rearranged.loc[idx, 'intensity'],
rearranged.loc[idx, 'response'],
bins='unique')
rearranged.loc[idx, 'sems'] = [
sum(rearranged.loc[idx, 'combinedN']) / n
for n in rearranged.loc[idx, 'combinedN']
] # sems is defined as 1/weight in Psychopy
guess = [5, 1]
rearranged.loc[idx, 'fit'] = FitCumNormal(
rearranged.loc[idx, 'combinedInten'],
rearranged.loc[idx, 'combinedResp'],
sems=rearranged.loc[idx, 'sems'],
guess=None,
expectedMin=0.0,
lapse=0.01) # customized cumulative Gaussian
rearranged.loc[idx,
'pse'] = rearranged.loc[idx,
'fit'].inverse(0.5 - .01)
rearranged.loc[idx,
'thre'] = rearranged.loc[idx,
'fit'].inverse(0.75 - .01)
return rearranged
def fitpf(self):
dfs, pool = self.sumxrl()
allIntensities = pool['allIntensities']
allResponses = pool['allResponses']
ntrial = pool['ntrial']
# curve fitting and plotting for each condition
res = {}
# print('label: ' + 'centre, ' + 'std, ' + 'ssq')
for idx, label in enumerate(allResponses.index):
res[label] = {}
res[label]['intensities'] = abs(allIntensities[label])
res[label]['responses'] = allResponses[label]
res[label]['combinedInten'], res[label]['combinedResp'], res[label]['combinedN'] = \
data.functionFromStaircase(res[label]['intensities'],
res[label]['responses'],
bins='unique') # bin data and fit to PF
res[label]['sems'] = [
1.0 / (n / sum(res[label]['combinedN']))
for n in res[label]['combinedN']
] # sems is defined as 1/weight in Psychopy
# res[label]['fit'] = data.FitCumNormal(res[label]['combinedInten'],
# res[label]['combinedResp'],
# sems=res[label]['sems'], guess=None,
# expectedMin=0.5) # cumulative Gaussian
guess = [5, 0.5]
# if label == 'hue_1p' or label == 'hue_2p':
# print('detected')
# guess = [8, 0.5]
res[label]['fit'] = FitCumNormal(
res[label]['combinedInten'],
res[label]['combinedResp'],
sems=res[label]['sems'],
guess=guess,
expectedMin=0.5,
lapse=0.05) # customized cumulative Gaussian
# print(label + ':' + str(res[label]['fit'].params) + ', ' + str(
# res[label]['fit'].ssq)) # a list with [centre, sd] for the Gaussian distribution forming the cumulative
res[label]['thresh'] = res[label]['fit'].inverse(0.75) # threshold
return ntrial, res
allIntensities.append(thisDat.intensities)
allResponses.append(thisDat.data)
#plot each staircase
pylab.subplot(121)
colors = 'brgkcmbrgkcm'
lines, names = [], []
for fileN, thisStair in enumerate(allIntensities):
#lines.extend(pylab.plot(thisStair))
#names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
#pylab.legend()
#get combined data
combinedInten, combinedResp, combinedN = \
data.functionFromStaircase(allIntensities, allResponses, 5)
#fit curve - in this case using a Weibull function
fit = data.FitFunction('weibullTAFC',combinedInten, combinedResp, \
guess=[0.2, 0.5])
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.8)
print thresh
#plot curve
pylab.subplot(122)
pylab.plot(smoothInt, smoothResp, '-')
pylab.plot([thresh, thresh], [0, 0.8], '--')pylab.plot([0, thresh],\
[0.8,0.8],'--')
pylab.title('threshold = %0.3f' % (thresh))
#plot points
#Act of importing will cause staircase intensities to log transform because that's how intensities are represented in the staircase
#staircase internal will be i = log(100-x)
#-(10**i)-100
staircase.importData( toStaircase(noiseEachTrial,descendingPsycho), np.array(corrEachTrial) )
printStaircase(staircase, briefTrialUpdate=False, printInternalVal=True, alsoLog=False)
#Fit and plot data
descendingPsycho = False
fit = None
intensityForCurveFitting = outOfStaircase(staircase.intensities,staircase,descendingPsycho)
#print('intensityForCurveFitting=',intensityForCurveFitting)
if descendingPsycho:
intensityForCurveFitting = 100-staircase.intensities #because fitWeibull assumes curve is ascending
#convert from list of trials to probabilities
combinedInten, combinedResp, combinedN = \
data.functionFromStaircase(intensityForCurveFitting, staircase.data, bins='unique')
print('combinedInten=',combinedInten,'combinedResp=',combinedResp)
try:
fit = data.FitWeibull(combinedInten, combinedResp, expectedMin=0, sems = 1.0/len(staircase.intensities))
print('fit=',fit)
except:
print("Fit failed.")
plotDataAndPsychometricCurve(staircase,fit,descendingPsycho,threshVal=0.75)
pylab.show() #must call this to actually show plot
testNoise = True
if testNoise: #Test noise
myWin = visual.Window()
proportnNoise = 0.9
noiseFieldWidthPix = 200
bgColor = [-.7,-.7,-.7]
for imageName, array in thisIndDat.extraInfo.iteritems():
thisImageName = imageName
indIntensities[thisImageName]=[]
indResponses[thisImageName]=[]
thisIntensity = thisIndDat.reversalIntensities[-10:]
thisResponse = thisIndDat.data[-10:]
indIntensities[thisImageName].extend(thisIntensity)
indResponses[thisImageName].extend(thisResponse)
#get individual data
thisNewIntensity = indIntensities[thisImageName]
thisNewResponse = indResponses[thisImageName]
combinedIndInten, combinedIndResp, CombinedN = data.functionFromStaircase(thisIntensity, thisResponse, 'unique')
#fit curve
combinedIndInten = numpy.array(combinedIndInten)+100
fit = data.FitWeibull(combinedIndInten, combinedIndResp, guess =[105, 10], expectedMin = 0.5)
smoothIndInt = pylab.arange(min(combinedIndInten), max(combinedIndInten), 0.001)
smoothIndResp = fit.eval(smoothIndInt)
Threshold = fit.inverse(0.8)-100
print 'Threshold', Threshold
label = thisImageName + (" - %.2f" %Threshold)
pylab.subplot(122)
pylab.plot(smoothIndInt-100, smoothIndResp, '--', label = label)
pylab.legend(loc = 'lower right')
assert isinstance(thisDat, data.StairHandler)
allIntensities.append(thisDat.intensities)
allResponses.append(thisDat.data)
# plot each staircase
pylab.subplot(121)
colors = "brgkcmbrgkcm"
lines, names = [], []
for fileN, thisStair in enumerate(allIntensities):
# lines.extend(pylab.plot(thisStair))
# names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
# pylab.legend()
# get combined data
combinedInten, combinedResp, combinedN = data.functionFromStaircase(allIntensities, allResponses, "unique")
combinedInten = np.asarray(combinedInten) + 100
# fit curve
fit = data.FitWeibull(combinedInten, combinedResp, guess=[100.2, 0.5], expectedMin=0.0)
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.5) - 100
# thresh = fit.inverse(0.8)-100
# lower = fit.inverse(0.675)
# upper = fit.inverse(0.925)
lower = fit.inverse(0.25) - 100
upper = fit.inverse(0.75) - 100
jnd = upper - lower
thisDat = fromFile(thisFileName)
assert isinstance(thisDat, data.StairHandler)
allIntensities.append( thisDat.intensities )
allResponses.append( thisDat.data )
# plot each staircase
pylab.subplot(121)
lines, names = [], []
for fileN, thisStair in enumerate(allIntensities):
# lines.extend(pylab.plot(thisStair))
# names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
# pylab.legend()
# get combined data
i, r, n = data.functionFromStaircase(allIntensities, allResponses, 'unique')
combinedInten, combinedResp, combinedN = i, r, n
# fit curve
guess =[num.average(combinedInten), num.average(combinedInten)/5]
fit = data.FitWeibull(combinedInten, combinedResp, guess=guess, expectedMin=0.0)
smoothInt = num.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.5)
print(thresh)
# plot curve
pylab.subplot(122)
pylab.plot(smoothInt, smoothResp, '-')
pylab.plot([thresh, thresh], [0, 0.5], '--')
xlimits=pylab.xlim([0,50])
ylimits=pylab.ylim([140,165])
pylab.subplot(212)
for fileN, thisStair in enumerate(allIntensitiesR):
pylab.plot(thisStair, '-')
pylab.title('%s_right_loc=%0.0f' %(thisOb,thisLocation))
xlimits=pylab.xlim([0,50])
ylimits=pylab.ylim([140,165])
pylab.savefig ('Analysis%s//FIGURES//SampleStaircases.png' %(fileTag), dpi = 600)
pylab.savefig ('Analysis%s//FIGURES//SampleStaircases.eps' %(fileTag), dpi = 600)
pylab.figure(2, figsize = (5,5))
#left side trials
combinedInten, combinedResp, combinedN = data.functionFromStaircase(allIntensitiesL, allResponsesL, 'unique')#fit curve
guess= [pylab.mean(combinedInten), 4.0]
fit = data.FitWeibull(combinedInten, combinedResp, expectedMin=0.0, guess=guess, display=0)
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.5)
lower = fit.inverse(0.25)
upper = fit.inverse(0.75)
jnd = upper - lower
#plot curve
pylab.plot(smoothInt, smoothResp, '-k')
pylab.plot([thresh, thresh],[0,0.5],'--r'); pylab.plot([0, thresh],[0.5,0.5],'--r')
#plot points
maxN=max(combinedN); minN=min(combinedN)
maxMarker=8.0; minMarker=4.0
for pointN in range(len(combinedInten)):
allRTs.append( thisDat.otherData['rt'])
#plot each staircase
pylab.subplot(131)
colors = 'brgkcmbrgkcm'
lines, names = [],[]
for fileN, thisStair in enumerate(allCoherenceLevels):
#lines.extend(pylab.plot(thisStair))
#names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
pylab.xlabel('Trial')
pylab.ylabel('Coherence')
#pylab.legend()
#get combined data
combinedInten, combinedResp, combinedN =data.functionFromStaircase(allCoherenceLevels, allResponses, 5)
#fit curve - in this case using a Weibull function
fit = data.FitWeibull(combinedInten, combinedResp, guess=[0.2, 0.5])
#smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothInt = pylab.arange(0.0, max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.8)
print thresh
#plot curve
pylab.subplot(132)
pylab.plot(smoothInt, smoothResp, '-')
pylab.plot([thresh, thresh],[0,0.8],'--')
pylab.plot([0, thresh], [0.8,0.8],'--')
pylab.title('threshold = %0.3f' % thresh)
#plot points
corrEachTrial = np.zeros( len(noiseEachTrial) )
for i in range( len(noiseEachTrial) ):
corrEachTrial[i] = np.random.binomial( 1, pCorrEachTrial[i] )
print('corrEachTrial=',corrEachTrial)
print('Importing responses ',np.array(corrEachTrial),' and intensities ',noiseEachTrial)
#Act of importing will cause staircase intensities to log transform because that's how intensities are represented in the staircase
#staircase internal will be i = log(100-x)
#-(10**i)-100
staircase.importData( toStaircase(noiseEachTrial,descendingPsycho), np.array(corrEachTrial) )
printStaircase(staircase, briefTrialUpdate=False, printInternalVal=True, alsoLog=False)
#Fit and plot data
descendingPsycho = False
fit = None
intensityForCurveFitting = outOfStaircase(staircase.intensities,staircase,descendingPsycho)
#print('intensityForCurveFitting=',intensityForCurveFitting)
if descendingPsycho:
intensityForCurveFitting = 100-staircase.intensities #because fitWeibull assumes curve is ascending
#convert from list of trials to probabilities
combinedInten, combinedResp, combinedN = \
data.functionFromStaircase(intensityForCurveFitting, staircase.data, bins='unique')
print('combinedInten=',combinedInten,'combinedResp=',combinedResp)
try:
fit = data.FitWeibull(combinedInten, combinedResp, expectedMin=0, sems = 1.0/len(staircase.intensities))
print('fit=',fit)
except:
print("Fit failed.")
plotDataAndPsychometricCurve(staircase,fit,descendingPsycho,threshVal=0.75)
pylab.show() #must call this to actually show plot
def fitpf(self):
from psychopy import data
import pylab
import matplotlib.pyplot as plt
dfs, _ = self.sumxrl()
allIntensities = dfs.groupby(level=0)['all_intensities'].apply(
np.hstack)
allResponses = dfs.groupby(level=0)['all_responses'].apply(np.hstack)
ntrial = dfs.groupby(level=0)['ntrial'].sum().unique()
num = int(len(allIntensities) / 2)
colorcodes = np.repeat(color4plot(num), 2, axis=0)
# curve fitting and plotting for each condition
fig, axes = plt.subplots(4, 4, figsize=(16, 10))
fig.suptitle(self.sub)
thresh = []
for idx, label in enumerate(allResponses.index):
intensities = abs(allIntensities[label])
responses = allResponses[label]
# bin data and fit to PF
combinedInten, combinedResp, combinedN = data.functionFromStaircase(
intensities, responses,
bins='unique') # optimal: bins='unique'
fit = data.FitCumNormal(combinedInten,
combinedResp,
guess=None,
expectedMin=0.5) # cumulative Gaussian
# fit = data.FitLogistic(combinedInten, combinedResp, guess=None) # logistic
# fit = data.FitWeibull(combinedInten, combinedResp, guess=[3, 0.5], display=1, expectedMin=0.5) #< --- somehow errors
thresh.append(fit.inverse(0.76)) # threshold
print(label + ': % 0.3f' % fit.ssq)
# plot
ax = axes.flatten()[idx]
fontsize = 8
ax.plot(combinedInten,
combinedResp,
'o',
fillstyle='none',
color='grey',
alpha=.5,
markersize=5) # plot combined data points
# ax.plot(intensities, responses, 'o', color='grey', alpha=.5, markersize=3) # plot all data points
# smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.1) # x for fitted curve
# smoothResp = fit.eval(smoothInt) # y for fitted curve
smoothResp = pylab.arange(0.5, 1, 0.02)
smoothInt = fit.inverse(smoothResp)
ax.plot(smoothInt, smoothResp, '-',
color=colorcodes[idx]) # plot fitted curve
ax.plot([thresh[idx], thresh[idx]], [0, 0.76], '--', color='grey')
ax.plot([0, thresh[idx]], [0.76, 0.76], '--', color='grey')
ax.set_title(label + ' ' + 'threshold = %0.3f' % thresh[idx],
fontsize=fontsize)
ax.set_ylim([0.5, 1])
ax.set_xlim([0, 6])
ax.tick_params(axis='both', which='major', labelsize=fontsize - 2)
plt.setp(axes[-1, :], xlabel='hue angle')
plt.setp(axes[:, 0], ylabel='correctness')
plt.savefig('pilot_data_fig/' + self.sub + '_' +
self.xstr(self.sel_par) + '_' + self.xstr(self.sel_ses) +
'_' + str(ntrial) + 'trl' + '.pdf')
plt.show()
return allResponses, thresh
def fitnoise(pool):
allIntensities = 10 - pool['allIntensities']
allResponses = pool['allResponses'] # reverse the response
ntrial = pool['ntrial']
# curve fitting and plotting for each condition
res = {}
# print('label: ' + 'centre, ' + 'std, ' + 'ssq')
fig, axes = plt.subplots(1, len(pool['allIntensities']), figsize=(8, 6))
fig.suptitle(str(ntrial) + 'trials')
for idx, label in enumerate(allResponses.index):
res[label] = {}
res[label]['intensities'] = allIntensities[label]
res[label]['responses'] = allResponses[label]
# plt.scatter(res[label]['intensities'], res[label]['responses'])
res[label]['combinedInten'], res[label]['combinedResp'], res[label]['combinedN'] = \
data.functionFromStaircase(res[label]['intensities'],
res[label]['responses'],
bins=5) # bin data and fit to PF
# plt.scatter(res[label]['combinedInten'], res[label]['combinedResp'])
res[label]['sems'] = [
1.0 / (n / sum(res[label]['combinedN']))
for n in res[label]['combinedN']
] # sems is defined as 1/weight in Psychopy
guess = [3, 0.5]
# if label == 'hue_1p' or label == 'hue_2p':
# print('detected')
# guess = [8, 0.5]
res[label]['fit'] = FitCumNormal(
res[label]['combinedInten'],
res[label]['combinedResp'],
sems=res[label]['sems'],
guess=None,
expectedMin=0.5,
lapse=0.01) # customized cumulative Gaussian
# print(label + ':' + str(res[label]['fit'].params) + ', ' + str(
# res[label]['fit'].ssq)) # a list with [centre, sd] for the Gaussian distribution forming the cumulative
res[label]['thresh'] = res[label]['fit'].inverse(0.76) # threshold
this_res = res[label]
# print(label + ':' + str(this_res['fit'].params) + ', ' + str(
# this_res['fit'].ssq)) # a list with [centre, sd] for the Gaussian distribution forming the cumulative
if len(pool['allIntensities']) > 1:
ax = axes.flatten()[idx]
else:
ax = axes
fontsize = 8
for inten, resp, se in zip(
this_res['combinedInten'], this_res['combinedResp'],
this_res['sems']): # plot combined data points
ax.plot(inten, resp, '.', alpha=0.5, markersize=300 / se)
smoothResp = pylab.arange(0.01, 0.99, .02)
smoothInt = this_res['fit'].inverse(smoothResp)
# smoothInt = pylab.arange(0, 6.0, 0.05)
# smoothResp = this_res['fit'].eval(smoothInt)
ax.plot(smoothInt, smoothResp, '-') # plot fitted curve
ax.plot([this_res['thresh'], this_res['thresh']], [0, 0.75],
'--',
color='grey')
ax.plot([0, this_res['thresh']], [0.75, 0.75], '--', color='grey')
ssq = np.round(this_res['fit'].ssq, decimals=3) # sum-squared error
thre_std = np.round(np.sqrt(np.diagonal(this_res['fit'].covar))[0],
decimals=3)
ax.text(3.5, 0.55, 'ssq = ' + str(ssq), fontsize=fontsize)
ax.text(3.5, 0.53, 'thre_error = ' + str(thre_std), fontsize=fontsize)
ax.set_title(label + ' ' + 'threshold = %0.3f' % this_res['thresh'],
fontsize=fontsize)
ax.set_ylim([0.5, 1])
# ax.set_xlim([0, 6])
ax.tick_params(axis='both', which='major', labelsize=fontsize - 2)
ax.set_xlabel('level of coherence (10 - std)')
ax.set_ylabel('correctness')
print(this_res['fit'].params[0], ' +/- ', thre_std)
plt.show()
allRTs[condition].append(rt)
if not coherence in coherence_resp[condition]:
coherence_resp[condition][coherence] = []
coherence_resp[condition][coherence].append(float(resp))
if not coherence in coherence_rt[condition]:
coherence_rt[condition][coherence] = []
coherence_rt[condition][coherence].append(rt)
perf_ax = pylab.subplot(121)
rt_ax = pylab.subplot(122)
for condition in coherence_resp:
# get combined data
combinedInten, combinedResp, combinedN = data.functionFromStaircase(
allCoherenceLevels[condition], allResponses[condition], 10
)
# combinedInten=coherence_resp.keys()
# combinedInten.sort()
# combinedResp=[np.mean(coherence_resp[x]) for x in combinedInten]
# combinedRT=[np.mean(coherence_rt[x]) for x in combinedInten]
# fit curve - in this case using a Weibull function
fit = data.FitWeibull(combinedInten, combinedResp, guess=[0.2, 0.5])
# smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothInt = pylab.arange(0.0, max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.8)
print thresh
# plot curve
allResponses.append(thisDat.data)
dataFolder = os.path.split(thisFileName)[0] # just the path, not file name
# plot each staircase in left hand panel
pylab.subplot(121)
colors = 'brgkcmbrgkcm'
lines, names = [], []
for fileN, thisStair in enumerate(allIntensities):
# lines.extend(pylab.plot(thisStair)) # uncomment for a legend for files
# names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
# pylab.legend()
# get combined data
i, r, n = data.functionFromStaircase(allIntensities,
allResponses,
bins='unique')
combinedInten, combinedResp, combinedN = i, r, n
combinedN = pylab.array(combinedN) # convert to array so we can do maths
# fit curve
fit = data.FitWeibull(combinedInten,
combinedResp,
expectedMin=expectedMin,
sems=1.0 / combinedN)
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(threshVal)
print(thresh)
# plot curve
allResponses.append( thisDat.loops[0].data )
dataFolder = os.path.split(thisFileName)[0] #just the path, excluding file name
#plot each staircase in left hand panel
pylab.subplot(121)
colors = 'brgkcmbrgkcm'
lines, names = [],[]
for fileN, thisStair in enumerate(allIntensities):
#lines.extend(pylab.plot(thisStair)) #uncomment these lines to get a legend for files
#names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
#pylab.legend()
#get combined data
combinedInten, combinedResp, combinedN = \
data.functionFromStaircase(allIntensities, allResponses, bins='unique')
combinedN = pylab.array(combinedN) #convert to array so we can do maths with them
#fit curve
fit = data.FitWeibull(combinedInten, combinedResp, expectedMin=expectedMin,
sems = 1.0/combinedN)
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(threshVal)
print thresh
#plot curve
pylab.subplot(122)
pylab.plot(smoothInt, smoothResp, 'k-')
pylab.plot([thresh, thresh],[0,threshVal],'k--') #vertical dashed line
pylab.plot([0, thresh],[threshVal,threshVal],'k--') #horizontal dashed line
allIntensities.append( thisDat.intensities )
allResponses.append( thisDat.data )
#plot each staircase
pylab.subplot(121)
colors = 'brgkcmbrgkcm'
lines, names = [],[]
for fileN, thisStair in enumerate(allIntensities):
#lines.extend(pylab.plot(thisStair))
#names = files[fileN]
pylab.plot(thisStair, label=files[fileN])
#pylab.legend()
#get combined data
combinedInten, combinedResp, combinedN = \
data.functionFromStaircase(allIntensities, allResponses, 5)
#fit curve
fit = data.FitWeibull(combinedInten, combinedResp, guess=[0.2, 0.5])
smoothInt = pylab.arange(min(combinedInten), max(combinedInten), 0.001)
smoothResp = fit.eval(smoothInt)
thresh = fit.inverse(0.8)
print thresh
#plot curve
pylab.subplot(122)
pylab.plot(smoothInt, smoothResp, 'k-')
pylab.plot([thresh, thresh],[0,0.8],'k--'); pylab.plot([0, thresh],[0.8,0.8],'k--')
pylab.title('threshold = %0.3f' %(thresh))
#plot points
pylab.plot(combinedInten, combinedResp, 'ko')
pylab.ylim([0,1])
def fitData(stairs, percent):
allIntensities, allResponses = [], []
for s in stairs.staircases:
allIntensities.append(s.intensities)
allResponses.append(s.data)
for s in stairs.staircases:
print "Mean for condition ", s.condition['label'], "=", average(
s.reversalIntensities), "std=", std(s.reversalIntensities)
#plot each condition
pylab.subplot(221)
#for stairNumber, thisStair in enumerate(allIntensities):
pylab.plot(allIntensities[0],
'o-',
label=stairs.staircases[0].condition['label'])
pylab.xlabel('Trials')
pylab.ylabel('Speed [cm/s]')
pylab.legend()
# Get combined data
combinedInten, combinedResp, combinedN = data.functionFromStaircase(
allIntensities, allResponses, 10)
# Fit curve - in this case using a Weibull function
fit = data.FitFunction('weibullTAFC',
combinedInten,
combinedResp,
guess=None)
#fit = data.FitCumNormal(combinedInten,combinedResp)
intensitiesDomainInterp = pylab.arange(min(allIntensities[0]),
max(allIntensities[0]), 0.01)
smoothResponses = fit.eval(intensitiesDomainInterp)
thresh = fit.inverse(percent)
#Plot fitted curve
pylab.subplot(222)
pylab.axis(xmin=min(allIntensities[0]), xmax=max(allIntensities[0]))
pylab.xlabel('Speed [cm/s]')
pylab.ylabel('Probability')
pylab.plot(intensitiesDomainInterp, smoothResponses, '-')
pylab.plot([thresh, thresh], [0, percent], '--')
pylab.plot([0, thresh], [percent, percent], '--')
pylab.title('Threshold at ' + str(percent) + '= %0.3f' % (thresh))
# Plot points
pylab.plot(combinedInten, combinedResp, 'o')
pylab.ylim([0, 1])
# SECOND CONDITION, the plots are in a second row, under
pylab.subplot(223)
#for stairNumber, thisStair in enumerate(allIntensities):
pylab.plot(allIntensities[1],
'o-',
label=stairs.staircases[1].condition['label'])
pylab.xlabel('Trials')
pylab.ylabel('Speed [cm/s]')
pylab.legend()
# Get combined data
combinedInten, combinedResp, combinedN = data.functionFromStaircase(
allIntensities[1], allResponses[1], 10)
#fit curve - in this case using a Weibull function
#fit = data.FitFunction('weibullTAFC',combinedInten, combinedResp, guess=None)
fit = data.FitCumNormal(combinedInten, combinedResp)
intensitiesDomainInterp = pylab.arange(min(allIntensities[1]),
max(allIntensities[1]), 0.01)
smoothResponses = fit.eval(intensitiesDomainInterp)
thresh = fit.inverse(percent)
#print "Threshold at " + str(percent) +"% with Cumulative Normal= ",thresh
#Plot fitted curve
pylab.subplot(224)
pylab.axis(xmin=min(allIntensities[1]), xmax=max(allIntensities[1]))
pylab.xlabel('Speed [cm/s]')
pylab.ylabel('Probability')
pylab.plot(intensitiesDomainInterp, smoothResponses, '-')
pylab.plot([thresh, thresh], [0, percent], '--')
pylab.plot([0, thresh], [percent, percent], '--')
pylab.title('Threshold at ' + str(percent) + '= %0.3f' % (thresh))
# Plot points
pylab.plot(combinedInten, combinedResp, 'o')
pylab.ylim([0, 1])
pylab.show()